Mercurial > repos > devteam > sam_pileup

annotate tool-data/fasta_indexes.loc.sample @ 2:3ff8935743a9 draft

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Remove unused flags from tool wrapper XML.
author devteam
date Thu, 09 Jan 2014 14:22:45 -0500
parents e7d863c5c5d6
children 890d97772e2a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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2 #to use a directory of Samtools indexed sequences data files. You will need
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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3 #to create these data files and then create a sam_fa_new_indices.loc file
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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4 #similar to this one (store it in this directory) that points to
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
5 #the directories in which those files are stored. The sam_fa_new_indices.loc
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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6 #file has this format (white space characters are TAB characters):
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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7 #
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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9 #
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
10 #So, for example, if you had hg19 Canonical indexed stored in
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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11 #
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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12 # /depot/data2/galaxy/hg19/sam/,
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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13 #
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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14 #then the sam_fa_new_indices.loc entry would look like this:
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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15 #
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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17 #
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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18 #and your /depot/data2/galaxy/hg19/sam/ directory
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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19 #would contain hg19canon.fa and hg19canon.fa.fai files.
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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20 #
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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21 #Your sam_fa_new_indices.loc file should include an entry per line for
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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22 #each index set you have stored. The file in the path does actually
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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23 #exist, but it should never be directly used. Instead, the name serves
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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24 #as a prefix for the index file. For example:
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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25 #
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
e7d863c5c5d6 Update sam_pileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa